TD Merchant Services offers EFT processing for cheques.
Moneris offers online EFT processing for CC info.
I haven't looked into it recently to see if one offers both yet. But Moneris can be setup for automatic withdraw every month, you can also freeze it and reactivate it whenever you'd like for specific clients. It does it all, but not for debit/bank accounts, only works on Credit Cards.
So one solution
is to only do EFT's with Credit Cards.
Moneris is around $35/month + the % per transaction, just like your Credit Card processing. TD Merchant services is around $50/month (for cheques only...not worth it)